# HG changeset patch # User chrisw # Date 1549996957 18000 # Node ID 1f0e3aaaba194990acfb39aec1b2d74092aefd18 Uploaded diff -r 000000000000 -r 1f0e3aaaba19 .shed.yml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/.shed.yml Tue Feb 12 13:42:37 2019 -0500 @@ -0,0 +1,11 @@ +categories: +- Statistics +description: bamcount is a tools for efficiently summarizing coverage information from a BAM file +long_description: | + bamcount is a tool for efficiently computing coverage statistics over a DNA/RNA BAM file. + It is aligner agnostic and counts everything over only one pass through the BAM. + https://github.com/BenLangmead/bamcount +name: bamcount +owner: ChristoperWilks +remote_repository_url: https://github.com/ChristopherWilks/bamcount_galaxy +type: unrestricted diff -r 000000000000 -r 1f0e3aaaba19 bamcount.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bamcount.xml Tue Feb 12 13:42:37 2019 -0500 @@ -0,0 +1,84 @@ + + + bamcount + + + + + + + + + + + + + + + [options] + + Options: + -h --help Show this screen. + --version Show version. + --threads # of threads to do BAM decompression + + Non-reference summaries: + --alts Print differing from ref per-base coverages + Writes to a CSV file .alts.tsv + --include-softclip Print a record for soft-clipped bases + --include-n Print mismatch records when mismatched read base is N + --print-qual Print quality values for mismatched bases + --delta Print POS field as +/- delta from previous + --require-mdz Quit with error unless MD:Z field exists everywhere it's + expected + --no-head Don't print sequence names and lengths in header + + Coverage and quantification: + --coverage Print per-base coverage (slow but totally worth it) + --auc Print per-base area-under-coverage, will generate it for the genome + and for the annotation if --annotation is also passed in + Writes to a TSV file .auc.tsv + --bigwig Output coverage as BigWig file(s). Writes to .all.bw + (also .unique.bw when --min-unique-qual is specified). + Requires libBigWig. + --annotation + Path to BED file containing list of regions to sum coverage over + (tab-delimited: chrm,start,end) + --min-unique-qual + Output second bigWig consisting built only from alignments + with at least this mapping quality. --bigwig must be specified. + Also produces second set of annotation sums based on this coverage + if --annotation is enabled + --double-count Allow overlapping ends of PE read to count twice toward + coverage + --num-bases Report total sum of bases in alignments processed (that pass filters) + + Other outputs: + --read-ends Print counts of read starts/ends, if --min-unique-qual is set + then only the alignments that pass that filter will be counted here + Writes to 2 TSV files: .starts.tsv, .ends.tsv + --frag-dist Print fragment length distribution across the genome + Writes to a TSV file .frags.tsv + --echo-sam Print a SAM record for each aligned read + --ends Report end coordinate for each read (useful for debugging) + ]]> + + +@misc{githubbamcount, + author = {Wilks, Christopher}, + year = {2019}, + title = {bamcount}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/BenLangmead/bamcount}, +} + + diff -r 000000000000 -r 1f0e3aaaba19 test-data/test.bam Binary file test-data/test.bam has changed diff -r 000000000000 -r 1f0e3aaaba19 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Feb 12 13:42:37 2019 -0500 @@ -0,0 +1,6 @@ + + + + + +